Align Glycine betaine/proline betaine transport system permease protein ProW (characterized)
to candidate AZOBR_RS23475 AZOBR_RS23475 glycine betaine transporter subunit ; membrane component of ABC superfamily
Query= SwissProt::P14176 (354 letters) >FitnessBrowser__azobra:AZOBR_RS23475 Length = 312 Score = 274 bits (700), Expect = 3e-78 Identities = 133/267 (49%), Positives = 184/267 (68%) Query: 62 IPLDSWVTEGIDWVVTHFRPVFQGVRVPVDYILNGFQQLLLGMPAPVAIIVFALIAWQIS 121 +P+ W + +++ H + +F G+ + V + +G Q L +P + LI + Sbjct: 5 LPIGDWADAAVMFLLDHAQWLFDGIDLVVGAVADGVQAALTALPGVALAAIVVLIGLWRN 64 Query: 122 GVGMGVATLVSLIAIGAIGAWSQAMVTLALVLTALLFCIVIGLPLGIWLARSPRAAKIIR 181 G + +L+ + +G W Q + TLALVLTA + IG+PLGI AR+ R ++R Sbjct: 65 GWRFALFAAAALMVVAGLGMWHQTVDTLALVLTATAIALTIGVPLGIVAARNDRVETVVR 124 Query: 182 PLLDAMQTTPAFVYLVPIVMLFGIGNVPGVVVTIIFALPPIIRLTILGINQVPADLIEAS 241 P LD MQT PAFVYL+P MLFG+G VPG++ TIIFA+PP++RLT LGI QVP +L+EA Sbjct: 125 PALDLMQTMPAFVYLIPAAMLFGLGRVPGIIATIIFAMPPVVRLTSLGIRQVPHELVEAG 184 Query: 242 RSFGASPRQMLFKVQLPLAMPTIMAGVNQTLMLALSMVVIASMIAVGGLGQMVLRGIGRL 301 +FG +PRQ+LFKVQ+P A+P+IMAG+NQT+ML+LSMVVIASMI GG+G VLRGI RL Sbjct: 185 LAFGCTPRQLLFKVQMPTALPSIMAGINQTIMLSLSMVVIASMIGAGGVGNEVLRGIQRL 244 Query: 302 DMGLATVGGVGIVILAIILDRLTQAVG 328 D+GL GG+ +VILAI+LDR+TQ+ G Sbjct: 245 DIGLGVEGGLAVVILAILLDRITQSFG 271 Lambda K H 0.326 0.141 0.435 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 352 Number of extensions: 15 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 354 Length of database: 312 Length adjustment: 28 Effective length of query: 326 Effective length of database: 284 Effective search space: 92584 Effective search space used: 92584 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory